Okay, I did run this by Ragnarokx our Moderator for Epic 4g and he said in theory it should work flashing a zip with the files your missing but he also remembers people having some issues in past updates doing this.
He recommended and I agree your best bet for a guaranteed OTA update is to Odin back to stock Froyo EB13 so you have no worries on missing the OTA update. You can't use the update.zip method, that is only going from Eclair 2.1 (DI18) to Froyo EB13.
Use procedure #1 in the link below to perform the process.
[How to] Factory Restore (or Fix a Bricked Phone)
Wow, alright. I kinda figured It'd be a bit more involved than simply just being able to re-install the missing .apk files, but thats what I get for being ******ed and not backing up the apps before I removed them. That said, thanks a bunch for the help. I will be doing this in the morning though, time for bed now.

EDIT: I just remembered that I also have the full Samsung installer app for EB13 as well. Would I be able to just use that instead to essentially re-flash the entire device back to stock EB13? Or is the Odin method in your guide the better/easier way to go?